Functional genomics will change knowledge and practice in clinical nutrition in the forthcoming years. The possibility of performing an individual's genetic profile (genetic variations and epigenetic modifications) as well as the ability of its integration in a complex network of metabolic interactions represents a huge challenge in Human Nutrition. The influence of nutrigenomics in terms of prevention and treatment of chronic diseases, such as obesity, type 2 diabetes and cardiovascular disease in a population level remains undetermined for the moment. The opportunity of nutritional intervention in critical stages of development and the chance of changing genetic susceptibility to diseases through diet in a Public Health basis should lead the future of nutrigenomics beyond the mere design of "personalized" functional food or diets.